Sir Alex Ferguson is facing the possibility of a minimum two-match touchline ban for his outspoken criticisms of the referee Martin Atkinson.

The Football Association's lawyers are deliberating over whether to open proceedings against the Manchester United manager following his reaction to the 2-1 defeat by Chelsea at Stamford Bridge. United have already spoken to their own legal advisers and Ferguson has indicated he intends to plead not guilty if he is to face disciplinary action for the fifth time in as many years.

The expectation within Old Trafford is that he will be charged and Ferguson already has two matches of a four-game touchline ban hanging over him as a suspended sentence for his condemnation of Alan Wiley in 2009 as not being physically fit to officiate in the Premier League.

That punishment will be triggered automatically if Ferguson is found guilty of misconduct for the post-match outburst in which he castigated Atkinson for not sending off the Chelsea defender David Luiz and blamed the defeat on a series of refereeing decisions.

"You hope you get a really strong referee in games like this," he said. "It was a major game for both clubs and you want a fair referee, you know ... You want a strong referee, anyway, and we didn't get that. I don't know why he's got the game. I must say that, when I saw who was refereeing it, I feared the worst."

The FA's investigation is heavily focused on the word "fair" and the implication that Ferguson was alleging lack of impartiality on the part of a referee who has been a source of frustration to him ever since an FA Cup tie against Portsmouth in March 2008, when both the United manager and his then assistant, Carlos Queiroz, were charged for their criticisms of his performance.

The FA has asked Sky and MUTV for an unedited copy of their post-match interviews from Stamford Bridge and the governing body has until 4pm on Friday to decide what to do next. In Ferguson's defence, the way he appears to backtrack a little on the "fair" comment may help him in what is considered a difficult and tight decision for the FA.

If charged, Ferguson would be given one working day to respond and a hearing would take place next week, ruling out the possibility that Ferguson will have to watch Sunday's game at Liverpool in the stands. Instead, a possible ban would come into place for two home games, the FA Cup quarter-final on 12 March and the Premier League game against Bolton Wanderers a week later.

In the case of a proven charge, the FA would also have the power to add to that punishment if it felt the offence was serious enough, and it would be held against Ferguson if he has chosen to deny any wrongdoing.

Alan Leighton, head of the referees' union, Prospect, called on Ferguson to retract his comments about Atkinson. "The ball is in Sir Alex's court," he said. "I'm less interested in whether he's charged than removing this stigma from the referee at Stamford Bridge.

"The referees are saying that if one is questioned then it questions them all. None of them want their integrity impaired. So the best way would be a retraction."

United's manager is facing problems in his back four for the match at Liverpool because Nemanja Vidic is suspended after being sent off at Chelsea and Rio Ferdinand and Jonny Evans are injured. It means Chris Smalling is likely to be partnered in central defence by Wes Brown, who has fallen out of favour and has not featured in the Premier League since November. The left-back Patrice Evra, meanwhile, is having treatment after coming off at Stamford Bridge with an injury.

Michael Carrick has called on United to react swiftly to their second defeat in four league games. "We feel pretty down but we can move on quickly," the midfielder said. "We have to. We're used to doing it and normally we are good at it. That is the nature of the beast."

• This article was amended on 3 March 2011. The original said Ferguson was alleging impartiality on the part of a referee. This has been corrected.